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- PDB-9eq7: Halobacterium salinarum archaellum filament -

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Basic information

Entry
Database: PDB / ID: 9eq7
TitleHalobacterium salinarum archaellum filament
ComponentsArchaellin
KeywordsSTRUCTURAL PROTEIN / archaellum / haloarcheon / archaellin
Biological speciesHalobacterium salinarum (Halophile)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.23 Å
AuthorsGrossman-Haham, I. / Shahar, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Perturbed N-glycosylation of Halobacterium salinarum archaellum filaments leads to filament bundling and compromised cell motility.
Authors: Shahar Sofer / Zlata Vershinin / Leen Mashni / Ran Zalk / Anat Shahar / Jerry Eichler / Iris Grossman-Haham /
Abstract: The swimming device of archaea-the archaellum-presents asparagine (N)-linked glycans. While N-glycosylation serves numerous roles in archaea, including enabling their survival in extreme ...The swimming device of archaea-the archaellum-presents asparagine (N)-linked glycans. While N-glycosylation serves numerous roles in archaea, including enabling their survival in extreme environments, how this post-translational modification contributes to cell motility remains under-explored. Here, we report the cryo-EM structure of archaellum filaments from the haloarchaeon Halobacterium salinarum, where archaellins, the building blocks of the archaellum, are N-glycosylated, and the N-glycosylation pathway is well-resolved. We further determined structures of archaellum filaments from two N-glycosylation mutant strains that generate truncated glycans and analyzed their motility. While cells from the parent strain exhibited unidirectional motility, the N-glycosylation mutant strain cells swam in ever-changing directions within a limited area. Although these mutant strain cells presented archaellum filaments that were highly similar in architecture to those of the parent strain, N-linked glycan truncation greatly affected interactions between archaellum filaments, leading to dramatic clustering of both isolated and cell-attached filaments. We propose that the N-linked tetrasaccharides decorating archaellins act as physical spacers that minimize the archaellum filament aggregation that limits cell motility.
History
DepositionMar 21, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Archaellin
B: Archaellin
C: Archaellin
D: Archaellin
E: Archaellin
F: Archaellin
G: Archaellin
H: Archaellin
I: Archaellin
J: Archaellin
K: Archaellin
L: Archaellin
M: Archaellin
N: Archaellin
O: Archaellin
P: Archaellin
Q: Archaellin
R: Archaellin
S: Archaellin
T: Archaellin
U: Archaellin
V: Archaellin
W: Archaellin
X: Archaellin
Y: Archaellin
Z: Archaellin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)567,97778
Polymers522,80726
Non-polymers45,17052
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Archaellin


Mass: 20107.971 Da / Num. of mol.: 26 / Source method: isolated from a natural source
Details: Since Hbt. salinarum encodes five archaellins (i.e., FlaA1, FlaA2, FlaB1, FlaB2, and FlaB3) and their arrangement within the archaellum filaments is unknown, we further refined the cryo-EM ...Details: Since Hbt. salinarum encodes five archaellins (i.e., FlaA1, FlaA2, FlaB1, FlaB2, and FlaB3) and their arrangement within the archaellum filaments is unknown, we further refined the cryo-EM map without applying symmetry, in an attempt to resolve the positions of these archaellins within the filament, as done previously with reconstruction of the Methanocaldococcus villosus archaellum. Symmetry-free refinement improved the overall resolution map to 3.1 A and revealed differences in density among archaellin subunits. Nonetheless, we were unable to identify features that would allow us to unambiguously assign specific archaellins into the density, perhaps because the regions that distinguish each archaellin are few, short, and mostly predicted to lack defined secondary structure, or because the five archaellins are not organized in a repeating pattern. Consequently, we built a model into the central region of the cryo-EM map comprising 26 archaellin subunits that share a consensus sequence, in which identical residues among the five archaellins are explicitly modelled, with those variable residues usually being modelled as alanine residues (UNK).
Source: (natural) Halobacterium salinarum (Halophile)
#2: Polysaccharide...
2-O-sulfo-beta-D-glucopyranuronic acid-(1-4)-3-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-beta-D- ...2-O-sulfo-beta-D-glucopyranuronic acid-(1-4)-3-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-beta-D-glucopyranuronic acid-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 868.655 Da / Num. of mol.: 52 / Source method: obtained synthetically
DescriptorTypeProgram
[]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-GlcpA]{[(4+1)][a-L-IdopA3SO3]{[(4+1)][b-D-GlcpA2SO3]{}}}}}LINUCSPDB-CARE
Compound detailsHalobacterium salinarum
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Archaellum filament / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.0215 MDa / Experimental value: NO
Source (natural)Organism: Halobacterium salinarum (Halophile)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1250 mg/mLSodium ChlorideNaCl1
220 mg/mLMagnesium SulfateMgSO4*7H2O1
33 mg/mLsodium citrateNa3C6H5O71
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: OTHER / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21rc1_4985: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 107.95 ° / Axial rise/subunit: 5.49 Å / Axial symmetry: C1
3D reconstructionResolution: 3.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 334202 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00336505
ELECTRON MICROSCOPYf_angle_d0.74850446
ELECTRON MICROSCOPYf_dihedral_angle_d7.3078024
ELECTRON MICROSCOPYf_chiral_restr0.0417029
ELECTRON MICROSCOPYf_plane_restr0.0035814

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